Methods and compositions using one-sided transposition

Abstract

Embodiments provided herein relate to methods and compositions for next generation sequencing. Some embodiments include the preparation of a template library from a target nucleic acid using one-sided transposition, sequencing the template library, and capturing the contiguity information.

1 .- 86 . (canceled) 
     
     
         87 . A method for capturing contiguity information of a double-stranded target nucleic acid, comprising:
 (a) providing a plurality of transposomes, each transposome comprising a transposase and a transposon nucleic acid, wherein the transposon nucleic acid comprises a double-stranded y-shaped adapter, and the transposase comprises an activity to nick only one strand of the double-stranded target nucleic acid;   (b) contacting the double-stranded target nucleic acid with the plurality of transposomes such that the double-stranded target nucleic acid is nicked at a plurality of sites and single transposon nucleic acids are attached to at least one of the nicked target nucleic acids to generate transposed nucleic acids; and   (c) sequencing the transposed nucleic acids; and   (d) identifying target nucleic acid sequences of the transposed nucleic acids having a shared property, thereby capturing the contiguity information.   
     
     
         88 . The method of  claim 87 , wherein the shared property comprises a transposon nucleic acid sequence. 
     
     
         89 . The method of  claim 87 , wherein the y-shaped adapter comprises a blocking moiety. 
     
     
         90 . The method of  claim 87 , wherein the plurality of transposomes is attached to a surface. 
     
     
         91 . The method of  claim 90 , wherein the surface comprises a plurality of beads. 
     
     
         92 . The method of  claim 87 , wherein step (b) further comprises removing the plurality of transposomes from the transposed nucleic acids. 
     
     
         93 . The method of  claim 87 , wherein step (b) further comprises extending the transposed nucleic acids to generate a plurality of extended nucleic acids comprising overlapping sequences in a linear representation of a single target nucleic acid. 
     
     
         94 . The method of  claim 93 , wherein the extending is performed in solution. 
     
     
         95 . The method of  claim 93 , wherein the linear representation of the target nucleic acid sequence comprises a haplotype representation. 
     
     
         96 . The method of  claim 93 , further comprising ligating a strand of the Y-shaped adapter to an extended strand of the extended nucleic acids. 
     
     
         97 . The method of  claim 93 , further comprising: amplifying the plurality of extended nucleic acids. 
     
     
         98 . A method for capturing contiguity information of a double-stranded target nucleic acid, comprising:
 (a) providing a plurality of transposomes, each transposome comprising a transposase and a transposon nucleic acid, wherein the transposon nucleic acid comprises a double-stranded y-shaped adapter, and the transposase comprises an activity to nick only one strand of the double-stranded target nucleic acid;   (b) contacting the double-stranded target nucleic acid with the plurality of transposomes such that the double-stranded target nucleic acid is nicked at a plurality of sites of the target nucleic acid, wherein each nicked site comprises a first end and a second end of a strand of the double-stranded target nucleic acid, and single transposon nucleic acids are attached to the first end of at least one of the nicked target nucleic acids to generate transposed nucleic acids;   (c) joining a strand of the Y-shaped adapters to the nicked strands of the double-stranded target nucleic acid at the second end of the nicked sites, to generate a plurality of modified nucleic acids which comprise overlapping sequences in a linear representation of a single target nucleic acid, thereby obtaining a library of nucleic acids;   (d) sequencing the plurality of modified nucleic acids; and   (e) identifying target nucleic acid sequences of the plurality of modified nucleic acids having a shared property, thereby capturing the contiguity information.   
     
     
         99 . The method of  claim 98 , wherein the shared property comprises a transposon nucleic acid sequence. 
     
     
         100 . The method of  claim 98 , wherein step (c) comprises: (i) ligating the strand of the Y-shaped adapters to the nicked strands at the other side of the nicked sites; or (ii) a click-chemistry reaction between the strand of the Y-shaped adapters to the nicked strands at the other side of the nicked sites. 
     
     
         101 . The method of  claim 98 , wherein the plurality of transposomes is attached to a surface. 
     
     
         102 . The method of  claim 101 , wherein the surface comprises a plurality of beads. 
     
     
         103 . The method of  claim 98 , wherein step (b) further comprises removing the plurality of transposomes from the transposed nucleic acids. 
     
     
         104 . The method of  claim 98 , wherein step (c) is performed in solution. 
     
     
         105 . The method of  claim 98 , wherein the linear representation of the target nucleic acid sequence comprises a haplotype representation. 
     
     
         106 . The method of  claim 98 , wherein the target nucleic acid comprises genomic DNA.